OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Molecular Evolution is 2. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-08-01 to 2025-08-01.)

Article	Citations
Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins	80
Correction: Analysis of Cancer-Resisting Evolutionary Adaptations in Wild Animals and Applications for Human Oncology	47
Correction: Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates	32
Prebiotic N-(2-Aminoethyl)-Glycine (AEG)-Assisted Synthesis of Proto-RNA?	28
Modified Metabolism and Response to UV Radiation: Gene Expression Variations Along an Elevational Gradient in the Asiatic Toad (Bufo gargarizans)	27
Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation	24
Unusual Evolution of Cephalopod Tryptophan Indole-Lyases	20
Learning from the Codon Table: Convergent Recoding Provides Novel Understanding on the Evolution of A-to-I RNA Editing	20
Scaling up Functional Analyses of the G Protein-Coupled Receptor Rhodopsin	19
Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation	18
An Ultimate Question for Functional A-to-I mRNA Editing: Why Not a Genomic G?	15
The Ancient Origins of Death Domains Support the ‘Original Sin’ Hypothesis for the Evolution of Programmed Cell Death	14
Odorant-Binding and Chemosensory Proteins in Fig Wasps: Evolutionary Insights From Comparative Studies	13
Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair	12
Post-Subfunctionalization Functions of HIF-1αA and HIF-1αB in Cyprinid Fish: Fine-Tuning Mitophagy and Apoptosis Regulation Under Hypoxic Stress	12
Organophosphorus Compound Formation Through the Oxidation of Reduced Oxidation State Phosphorus Compounds on the Hadean Earth	11
Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions	11
Phylogenetic and Evolutionary Analysis of Plant Small RNA 2′-O-Methyltransferase (HEN1) Protein Family	11
On Protein Loops, Prior Molecular States and Common Ancestors of Life	11
dN/dS-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution	10
Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians	9
Detecting Selection on Segregating Gene Duplicates in a Population	9
Biochemical Property Based Positional Matrix: A New Approach Towards Genome Sequence Comparison	9
On the Nature of the Last Common Ancestor: A Story from its Translation Machinery	9
A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet	8

Functional Diversity of the Lepidopteran ATP-Binding Cassette Transporters	8
Pheromone Gene Diversification and the Evolution of Courtship Glands in Plethodontid Salamanders	8
Informatic Capabilities of Translation and Its Implications for the Origins of Life	8
RNA or DNA? Revisiting the Chemical Nature of the Cenancestral Genome	8
Possible Acquisition and Molecular Evolution of vpu Genes Inferred from Comprehensive Sequence Analysis of Human and Simian Immunodeficiency Viruses	8
Adaptation and Exaptation: From Small Molecules to Feathers	8
The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA	8
GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences	8
Conservation of Protein Kinase A Substrates in the Cnidarian Coral Spermatozoa Among Animals and Their Molecular Evolution	8
Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea	8
The De Novo Emergence of Two Brain Genes in the Human Lineage Appears to be Unsupported	8
Evolution and Functional Diversification of Serine Racemase Homologs in Bacteria	8
Biothermodynamics of Hemoglobin and Red Blood Cells: Analysis of Structure and Evolution of Hemoglobin and Red Blood Cells, Based on Molecular and Empirical Formulas, Biosynthesis Reactions, and Therm	7
Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes	7
A New View of the Last Universal Common Ancestor	7
A Law of Redundancy Compounds the Problem of Cancer and Precision Medicine	7
PAReTT: A Python Package for the Automated Retrieval and Management of Divergence Time Data from the TimeTree Resource for Downstream Analyses	7
Promiscuous Domains in Eukaryotes and HAT Proteins in FUNGI Have Followed Different Evolutionary Paths	7
EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids	6
FEZF2 and AIRE1: An Evolutionary Trade-off in the Elimination of Auto-reactive T Cells in the Thymus	6
Correction: Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	6
Costly circRNAs, Effective Population Size, and the Origins of Molecular Complexity	6
Correction: Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation–Drift Equilibrium	6
Analysis of the MCTP Amino Acid Sequence Reveals the Conservation of Putative Calcium- and Lipid-Binding Pockets Within the C2 Domains In Silico	6
Main Factors Shaping Amino Acid Usage Across Evolution	6
Putative MutS2 Homologs in Algae: More Goods in Shopping Bag?	6
Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1	6
Context-Dependent Mutation Dynamics, Not Selection, Explains the Codon Usage Bias of Most Angiosperm Chloroplast Genes	6
Origins and Functional Significance of Eukaryotic Protein Folds	6
Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	6
Caspase Domain Duplication During the Evolution of Caspase-16	6
Evolutionary Nonindependence Between Human piRNAs and Their Potential Target Sites in Protein-Coding Genes	5
The Mystery of Cancer Resistance: A Revelation Within Nature	5
Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes	5
APGW/AKH Precursor from Rotifer Brachionus plicatilis and the DNA Loss Model Explain Evolutionary Trends of the Neuropeptide LWamide, APGWamide, RPCH, AKH, ACP, CRZ, and GnRH Families	5
Transposable Element Diversity Remains High in Gigantic Genomes	5
Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics?	5
Jump-Chain Simulation of Markov Substitution Processes Over Phylogenies	5
Selection Pressure Regulates the Evolution-Structure–Function Paradigm of Monocyte Chemoattractant Protein Family	5
Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species	5
2022 Zuckerkandl Prize	5
A Genomic Conceptualization of Species	4
Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway	4
Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups	4
Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals	4
Phylogenetic and Ancestral Sequence Reconstruction of SARS-CoV-2 Reveals Latent Capacity to Bind Human ACE2 Receptor	4
Origin of Sex-Biased Mental Disorders: Do Males and Females Experience Different Selective Regimes?	4
How Many Factors Influence Genomic GC Content Among Prokaryotes?	4
A Simple Evolutionary Model of Genetic Robustness After Gene Duplication	4
Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage	4

2024 Zuckerkandl Prize	4
The Role of Selection and Migration in the Evolution of (Auto)Immunity Genes	4
Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	4
Epistasis-Driven Evolution of the SARS-CoV-2 Secondary Structure	3
A Concept of Complementarity Between Complexity and Redundancy can Account for Kant’s Biological Teleology and Unify Mechanistic and Finalistic Biology	3
In Memoriam of Giorgio Bernardi and Noboru Sueoka: A Personal View	3
Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes	3
Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited	3
Evolution of the Cytokinin Dehydrogenase (CKX) Domain	3
Decay of Skin-Specific Gene Modules in Pangolins	3
Varying Modes of Selection Among Toxin Families in the Venoms of the Giant Desert Hairy Scorpions (Hadrurus)	3
The Abundance of Viroid-Like RNA Obelisk-S.s in Streptococcus sanguinis SK36 May Suffice for Evolutionary Persistence	3
The Hypervariable Tpr Multigene Family of Theileria Parasites, Defined by a Conserved, Membrane-Associated, C-Terminal Domain, Includes Several Copies with Defined Orthology Between Species	3
Introduction to the Special Issue on Early Evolution and the Last Common Ancestor	3
Recurrent Independent Pseudogenization Events of the Sperm Fertilization Gene ZP3r in Apes and Monkeys	3
Evolution of the Major Components of Innate Immunity in Animals	3
On the Unknown Proteins of Eukaryotic Proteomes	3
Correction: G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases	3
Structural Computational Analysis of the Natural History of Class I aminoacyl-tRNA Synthetases Suggests their Role in Establishing the Genetic Code	3
A Comparative Genomics Approach to Understanding the Evolution of Olfaction in Cetaceans	3
The Unfinished Reconstructed Nature of the Last Universal Common Ancestor	3
Selection Across the Three-Dimensional Structure of Venom Proteins from North American Scolopendromorph Centipedes	3
Convergent Evolution of Two Dopamine Receptor Genes: Repeated Evolution of Exon 6 Skipping in Drd2, and Repeated Deletion of Exon 6 in Drd3	3
The Evolution of Hemocyanin Genes in Caenogastropoda: Gene Duplications and Intron Accumulation in Highly Diverse Gastropods	3
Revisiting the Design of the Long-Term Evolution Experiment with Escherichia coli	2
Ancestral Information Analysis of Chinese Korean Ethnic Group via a Novel Multiplex DIP System	2
Analysis of Programmed Cell Death-1 (PD-1) Gene Variations (re11568821 and rs41386349) in HTLV-1 Infection Using One Primer Pair and Proviral Load	2
Mutations Inactivating Biosynthesis of Dispensable Carbohydrate-Antigens Prevented Extinctions in Primate/Human Lineage Evolution	2
Expansion and Functional Diversification of Long-Wavelength-Sensitive Opsin in Anabantoid Fishes	2
Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host	2
A New Perspective on the Maillard Reaction and the Origin of Life	2
Human Riboviruses: A Comprehensive Study	2
Functional Diversification and the Plant Secondary Cell Wall	2
Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays	2
Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch	2
Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations	2
The Amphibian Major Histocompatibility Complex—A Review and Future Outlook	2
Conservation of a Chromosome 8 Inversion and Exon Mutations Confirm Common Gulonolactone Oxidase Gene Evolution Among Primates, Including H. Neanderthalensis	2
Codon Usage Bias: An Endless Tale	2
Positive Selection Shapes Breast Cancer Tumor Suppressor Genes: Unveiling Insights into BRCA1, BRCA2, and MDC1 Stability	2
Variables Influencing Differences in Sequence Conservation in the Fission Yeast Schizosaccharomyces pombe	2
Best Practices in Microbial Experimental Evolution	2
uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response	2
Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors	2
Structural and Evolutionary Analysis of Proteins Endowed with a Nucleotidyltransferase, or Non-canonical Palm, Catalytic Domain	2
nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models	2
Left–Right Reversal Recurrently Evolved Regardless of Diaphanous-Related Formin Gene Duplication or Loss in Snails	2
Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere	2
Nucleobases in Meteorites to Nucleobases in RNA and DNA?	2
Correction to: Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	2